Starting phenix.real_space_refine on Fri Mar 6 18:21:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7tb8_25794/03_2026/7tb8_25794.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tb8_25794/03_2026/7tb8_25794.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.83 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7tb8_25794/03_2026/7tb8_25794.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tb8_25794/03_2026/7tb8_25794.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7tb8_25794/03_2026/7tb8_25794.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tb8_25794/03_2026/7tb8_25794.map" } resolution = 2.83 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.013 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 145 5.16 5 C 21113 2.51 5 N 5515 2.21 5 O 6457 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 42 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 33230 Number of models: 1 Model: "" Number of chains: 23 Chain: "A" Number of atoms: 8492 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1085, 8492 Classifications: {'peptide': 1085} Link IDs: {'PTRANS': 54, 'TRANS': 1030} Chain breaks: 6 Chain: "B" Number of atoms: 8513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1088, 8513 Classifications: {'peptide': 1088} Link IDs: {'PTRANS': 55, 'TRANS': 1032} Chain breaks: 4 Chain: "C" Number of atoms: 8514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1088, 8514 Classifications: {'peptide': 1088} Link IDs: {'PTRANS': 55, 'TRANS': 1032} Chain breaks: 4 Chain: "D" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 973 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 2, 'TRANS': 123} Chain: "E" Number of atoms: 813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 813 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 100} Chain: "F" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 973 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 2, 'TRANS': 123} Chain: "G" Number of atoms: 813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 813 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 100} Chain: "H" Number of atoms: 932 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 122, 932 Classifications: {'peptide': 122} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 118} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "L" Number of atoms: 819 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 107, 819 Classifications: {'peptide': 107} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 99} Chain: "J" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 973 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 2, 'TRANS': 123} Chain: "K" Number of atoms: 813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 813 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 100} Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "B" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "C" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Time building chain proxies: 6.76, per 1000 atoms: 0.20 Number of scatterers: 33230 At special positions: 0 Unit cell: (159.759, 183.33, 236.583, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 145 16.00 O 6457 8.00 N 5515 7.00 C 21113 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=50, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.04 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.02 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.04 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.02 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.04 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.02 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.04 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.05 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.04 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.02 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.02 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.02 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 88 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 96 " distance=2.03 Simple disulfide: pdb=" SG CYS G 23 " - pdb=" SG CYS G 88 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS H 97 " - pdb=" SG CYS H 100B" distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 96 " distance=2.04 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-3 " NAG M 1 " - " NAG M 2 " BETA1-4 " NAG I 1 " - " NAG I 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " NAG-ASN " NAG A1301 " - " ASN A 282 " " NAG A1302 " - " ASN A 657 " " NAG A1303 " - " ASN A 616 " " NAG A1304 " - " ASN A 801 " " NAG A1305 " - " ASN A 709 " " NAG A1306 " - " ASN A1074 " " NAG A1307 " - " ASN A 603 " " NAG B1301 " - " ASN B 282 " " NAG B1302 " - " ASN B 616 " " NAG B1303 " - " ASN B 709 " " NAG B1304 " - " ASN B1074 " " NAG B1305 " - " ASN B 331 " " NAG C1301 " - " ASN C 331 " " NAG C1303 " - " ASN C 657 " " NAG C1304 " - " ASN C 616 " " NAG C1305 " - " ASN C1074 " " NAG C1306 " - " ASN C 61 " " NAG C1307 " - " ASN C 17 " " NAG C1308 " - " ASN C1134 " " NAG C1309 " - " ASN C1098 " " NAG C1310 " - " ASN C 801 " " NAG C1311 " - " ASN C 709 " " NAG C1312 " - " ASN C 234 " " NAG C1313 " - " ASN C 165 " " NAG I 1 " - " ASN A 331 " " NAG M 1 " - " ASN A1134 " " NAG N 1 " - " ASN A1098 " " NAG O 1 " - " ASN A 717 " " NAG P 1 " - " ASN B1134 " " NAG Q 1 " - " ASN B1098 " " NAG R 1 " - " ASN B 717 " " NAG S 1 " - " ASN B 801 " " NAG T 1 " - " ASN C 717 " Time building additional restraints: 2.43 Conformation dependent library (CDL) restraints added in 1.2 seconds 8278 Ramachandran restraints generated. 4139 Oldfield, 0 Emsley, 4139 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7786 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 78 sheets defined 16.9% alpha, 27.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.58 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 365 through 370 removed outlier: 3.562A pdb=" N TYR A 369 " --> pdb=" O TYR A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 3.991A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.516A pdb=" N GLN A 762 " --> pdb=" O SER A 758 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLU A 773 " --> pdb=" O GLY A 769 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N GLN A 774 " --> pdb=" O ILE A 770 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LYS A 776 " --> pdb=" O VAL A 772 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 912 through 918 removed outlier: 4.036A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 removed outlier: 3.661A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 946 through 965 removed outlier: 3.977A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 984 removed outlier: 3.548A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 3.913A pdb=" N GLU A 990 " --> pdb=" O PRO A 986 " (cutoff:3.500A) removed outlier: 5.813A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 4.972A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ILE A 993 " --> pdb=" O ALA A 989 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1148 removed outlier: 4.672A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 383 through 387 Processing helix chain 'B' and resid 418 through 423 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.598A pdb=" N GLN B 762 " --> pdb=" O SER B 758 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLN B 774 " --> pdb=" O ILE B 770 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 886 through 890 removed outlier: 3.571A pdb=" N GLY B 889 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 913 through 918 Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.719A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N SER B 940 " --> pdb=" O ASP B 936 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N THR B 941 " --> pdb=" O SER B 937 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.684A pdb=" N GLN B 949 " --> pdb=" O LEU B 945 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 5.081A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLY B 999 " --> pdb=" O ARG B 995 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1148 removed outlier: 4.166A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 365 through 371 removed outlier: 4.052A pdb=" N TYR C 369 " --> pdb=" O TYR C 365 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N SER C 371 " --> pdb=" O VAL C 367 " (cutoff:3.500A) Processing helix chain 'C' and resid 386 through 390 removed outlier: 3.785A pdb=" N ASP C 389 " --> pdb=" O LYS C 386 " (cutoff:3.500A) Processing helix chain 'C' and resid 633 through 638 removed outlier: 3.741A pdb=" N THR C 638 " --> pdb=" O VAL C 635 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.789A pdb=" N GLN C 762 " --> pdb=" O SER C 758 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 890 Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 912 through 918 removed outlier: 4.003A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.662A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 946 through 965 removed outlier: 3.727A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 5.218A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 5.170A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLU C1017 " --> pdb=" O ILE C1013 " (cutoff:3.500A) Processing helix chain 'C' and resid 1141 through 1147 Processing helix chain 'J' and resid 28 through 32 removed outlier: 3.821A pdb=" N SER J 31 " --> pdb=" O THR J 28 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N TYR J 32 " --> pdb=" O PHE J 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 28 through 32' Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 4.319A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ALA A 264 " --> pdb=" O THR A 95 " (cutoff:3.500A) removed outlier: 5.791A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) removed outlier: 9.488A pdb=" N HIS A 207 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 9.167A pdb=" N LEU A 223 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 4.021A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) removed outlier: 5.694A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.671A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 83 through 85 removed outlier: 5.737A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 83 through 85 removed outlier: 7.563A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 126 through 129 removed outlier: 3.610A pdb=" N VAL A 126 " --> pdb=" O SER A 172 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 311 through 319 removed outlier: 6.960A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 325 through 326 removed outlier: 3.788A pdb=" N ASN A 542 " --> pdb=" O ILE A 326 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 335 through 336 Processing sheet with id=AB1, first strand: chain 'A' and resid 356 through 358 Processing sheet with id=AB2, first strand: chain 'A' and resid 356 through 358 Processing sheet with id=AB3, first strand: chain 'A' and resid 565 through 566 removed outlier: 7.048A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'A' and resid 575 through 577 Processing sheet with id=AB5, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.191A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.585A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 702 through 704 Processing sheet with id=AB7, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.772A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N MET A1050 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.976A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.772A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.663A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 787 through 790 removed outlier: 5.704A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AC3, first strand: chain 'B' and resid 29 through 30 Processing sheet with id=AC4, first strand: chain 'B' and resid 36 through 37 removed outlier: 7.148A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 8.703A pdb=" N ALA B 222 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N HIS B 207 " --> pdb=" O ALA B 222 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ASN B 188 " --> pdb=" O GLU B 96 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLU B 96 " --> pdb=" O ASN B 188 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.913A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 66 through 67 removed outlier: 3.638A pdb=" N ALA B 67 " --> pdb=" O ALA B 263 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 84 through 85 removed outlier: 4.290A pdb=" N GLY B 107 " --> pdb=" O ARG B 237 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 126 through 129 removed outlier: 3.886A pdb=" N VAL B 126 " --> pdb=" O SER B 172 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N SER B 172 " --> pdb=" O VAL B 126 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 133 through 134 removed outlier: 3.606A pdb=" N SER B 162 " --> pdb=" O GLN B 134 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 153 through 156 removed outlier: 5.572A pdb=" N GLU B 154 " --> pdb=" O TYR B 144 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N TYR B 144 " --> pdb=" O GLU B 154 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N GLU B 156 " --> pdb=" O GLY B 142 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N LEU B 141 " --> pdb=" O LEU B 244 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 311 through 319 removed outlier: 7.025A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.960A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLY B 648 " --> pdb=" O THR B 645 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 377 through 380 Processing sheet with id=AD4, first strand: chain 'B' and resid 391 through 392 removed outlier: 3.979A pdb=" N VAL B 524 " --> pdb=" O PHE B 392 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 538 through 543 removed outlier: 3.716A pdb=" N ILE B 587 " --> pdb=" O ASP B 574 " (cutoff:3.500A) removed outlier: 5.479A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.075A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.625A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 701 through 704 removed outlier: 6.498A pdb=" N ALA B 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) removed outlier: 7.981A pdb=" N LYS C 790 " --> pdb=" O ALA B 701 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N ASN B 703 " --> pdb=" O LYS C 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD7 Processing sheet with id=AD8, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.576A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLY B1059 " --> pdb=" O ALA B1056 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.872A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.576A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.600A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.643A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 28 through 30 Processing sheet with id=AE4, first strand: chain 'C' and resid 36 through 37 removed outlier: 7.111A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 5.943A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.871A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.909A pdb=" N GLY C 107 " --> pdb=" O ARG C 237 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N ALA C 243 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N ILE C 101 " --> pdb=" O ALA C 243 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 84 through 85 removed outlier: 12.630A pdb=" N PHE C 238 " --> pdb=" O PHE C 135 " (cutoff:3.500A) removed outlier: 12.377A pdb=" N ASN C 137 " --> pdb=" O PHE C 238 " (cutoff:3.500A) removed outlier: 9.914A pdb=" N THR C 240 " --> pdb=" O ASN C 137 " (cutoff:3.500A) removed outlier: 5.098A pdb=" N LEU C 242 " --> pdb=" O PRO C 139 " (cutoff:3.500A) removed outlier: 9.095A pdb=" N GLN C 134 " --> pdb=" O ASN C 164 " (cutoff:3.500A) removed outlier: 8.002A pdb=" N ASN C 164 " --> pdb=" O GLN C 134 " (cutoff:3.500A) removed outlier: 8.585A pdb=" N CYS C 136 " --> pdb=" O SER C 162 " (cutoff:3.500A) removed outlier: 10.423A pdb=" N SER C 162 " --> pdb=" O CYS C 136 " (cutoff:3.500A) removed outlier: 10.271A pdb=" N ASP C 138 " --> pdb=" O TYR C 160 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N TYR C 160 " --> pdb=" O ASP C 138 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 119 through 121 Processing sheet with id=AE9, first strand: chain 'C' and resid 310 through 319 removed outlier: 5.553A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.506A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 396 through 398 removed outlier: 4.724A pdb=" N TYR C 396 " --> pdb=" O SER C 514 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N VAL C 512 " --> pdb=" O ASP C 398 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 654 through 660 removed outlier: 6.119A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.557A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 9.051A pdb=" N VAL C 656 " --> pdb=" O THR C 696 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.694A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.862A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.568A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AF6, first strand: chain 'C' and resid 1094 through 1097 Processing sheet with id=AF7, first strand: chain 'D' and resid 3 through 7 Processing sheet with id=AF8, first strand: chain 'D' and resid 58 through 60 removed outlier: 3.535A pdb=" N TYR D 59 " --> pdb=" O VAL D 50 " (cutoff:3.500A) removed outlier: 4.999A pdb=" N TRP D 47 " --> pdb=" O ARG D 38 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N ARG D 38 " --> pdb=" O TRP D 47 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N VAL D 116 " --> pdb=" O ARG D 98 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'D' and resid 58 through 60 removed outlier: 3.535A pdb=" N TYR D 59 " --> pdb=" O VAL D 50 " (cutoff:3.500A) removed outlier: 4.999A pdb=" N TRP D 47 " --> pdb=" O ARG D 38 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N ARG D 38 " --> pdb=" O TRP D 47 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'D' and resid 102 through 104 Processing sheet with id=AG2, first strand: chain 'E' and resid 4 through 7 Processing sheet with id=AG3, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.899A pdb=" N VAL E 11 " --> pdb=" O GLU E 105 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N TRP E 35 " --> pdb=" O LEU E 47 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N TYR E 49 " --> pdb=" O SER E 53 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'F' and resid 3 through 7 Processing sheet with id=AG5, first strand: chain 'F' and resid 58 through 60 removed outlier: 7.067A pdb=" N TRP F 36 " --> pdb=" O VAL F 48 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N VAL F 50 " --> pdb=" O PHE F 34 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N PHE F 34 " --> pdb=" O VAL F 50 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N VAL F 116 " --> pdb=" O ARG F 98 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'F' and resid 58 through 60 removed outlier: 7.067A pdb=" N TRP F 36 " --> pdb=" O VAL F 48 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N VAL F 50 " --> pdb=" O PHE F 34 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N PHE F 34 " --> pdb=" O VAL F 50 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'F' and resid 102 through 104 Processing sheet with id=AG8, first strand: chain 'G' and resid 4 through 7 removed outlier: 4.152A pdb=" N ASP G 70 " --> pdb=" O TYR G 67 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N TYR G 67 " --> pdb=" O ASP G 70 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'G' and resid 10 through 13 removed outlier: 3.511A pdb=" N VAL G 11 " --> pdb=" O ARG G 103 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'G' and resid 53 through 54 removed outlier: 6.700A pdb=" N TRP G 35 " --> pdb=" O LEU G 47 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N TYR G 49 " --> pdb=" O LEU G 33 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N LEU G 33 " --> pdb=" O TYR G 49 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AH3, first strand: chain 'H' and resid 18 through 19 Processing sheet with id=AH4, first strand: chain 'H' and resid 34 through 38 removed outlier: 3.941A pdb=" N GLY H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.557A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'H' and resid 93 through 94 removed outlier: 3.549A pdb=" N ALA H 94 " --> pdb=" O ILE H 102 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N ILE H 102 " --> pdb=" O ALA H 94 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH5 Processing sheet with id=AH6, first strand: chain 'L' and resid 10 through 12 removed outlier: 5.747A pdb=" N LEU L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH6 Processing sheet with id=AH7, first strand: chain 'L' and resid 20 through 24 Processing sheet with id=AH8, first strand: chain 'L' and resid 42 through 49 removed outlier: 5.207A pdb=" N ALA L 43 " --> pdb=" O LYS L 39 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N LYS L 39 " --> pdb=" O ALA L 43 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N LEU L 47 " --> pdb=" O TRP L 35 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 5.949A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'J' and resid 3 through 7 removed outlier: 3.604A pdb=" N VAL J 5 " --> pdb=" O ALA J 23 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'J' and resid 58 through 60 removed outlier: 7.137A pdb=" N TRP J 36 " --> pdb=" O VAL J 48 " (cutoff:3.500A) removed outlier: 5.353A pdb=" N VAL J 50 " --> pdb=" O PHE J 34 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N PHE J 34 " --> pdb=" O VAL J 50 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'J' and resid 102 through 104 Processing sheet with id=AI3, first strand: chain 'K' and resid 4 through 7 Processing sheet with id=AI4, first strand: chain 'K' and resid 10 through 12 removed outlier: 3.635A pdb=" N VAL K 11 " --> pdb=" O ARG K 103 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'K' and resid 35 through 37 removed outlier: 6.576A pdb=" N TRP K 35 " --> pdb=" O LEU K 47 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LYS K 45 " --> pdb=" O GLN K 37 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'K' and resid 89 through 90 removed outlier: 3.502A pdb=" N GLN K 90 " --> pdb=" O THR K 97 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N THR K 97 " --> pdb=" O GLN K 90 " (cutoff:3.500A) No H-bonds generated for sheet with id=AI6 1092 hydrogen bonds defined for protein. 2970 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.12 Time building geometry restraints manager: 3.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 10626 1.35 - 1.47: 8801 1.47 - 1.59: 14381 1.59 - 1.72: 1 1.72 - 1.84: 188 Bond restraints: 33997 Sorted by residual: bond pdb=" CB PRO B 809 " pdb=" CG PRO B 809 " ideal model delta sigma weight residual 1.492 1.639 -0.147 5.00e-02 4.00e+02 8.64e+00 bond pdb=" C1 NAG B1304 " pdb=" O5 NAG B1304 " ideal model delta sigma weight residual 1.406 1.441 -0.035 2.00e-02 2.50e+03 3.07e+00 bond pdb=" C1 NAG C1305 " pdb=" O5 NAG C1305 " ideal model delta sigma weight residual 1.406 1.441 -0.035 2.00e-02 2.50e+03 3.04e+00 bond pdb=" C1 NAG C1310 " pdb=" O5 NAG C1310 " ideal model delta sigma weight residual 1.406 1.440 -0.034 2.00e-02 2.50e+03 2.88e+00 bond pdb=" C1 NAG A1306 " pdb=" O5 NAG A1306 " ideal model delta sigma weight residual 1.406 1.439 -0.033 2.00e-02 2.50e+03 2.71e+00 ... (remaining 33992 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.07: 45416 2.07 - 4.15: 753 4.15 - 6.22: 63 6.22 - 8.29: 12 8.29 - 10.37: 3 Bond angle restraints: 46247 Sorted by residual: angle pdb=" CA PRO B 809 " pdb=" N PRO B 809 " pdb=" CD PRO B 809 " ideal model delta sigma weight residual 112.00 101.63 10.37 1.40e+00 5.10e-01 5.48e+01 angle pdb=" C SER K 30 " pdb=" CA SER K 30 " pdb=" CB SER K 30 " ideal model delta sigma weight residual 116.34 110.67 5.67 1.40e+00 5.10e-01 1.64e+01 angle pdb=" C GLN A 613 " pdb=" N ASP A 614 " pdb=" CA ASP A 614 " ideal model delta sigma weight residual 121.54 128.15 -6.61 1.91e+00 2.74e-01 1.20e+01 angle pdb=" CA GLY C 89 " pdb=" C GLY C 89 " pdb=" N VAL C 90 " ideal model delta sigma weight residual 115.34 118.19 -2.85 8.40e-01 1.42e+00 1.15e+01 angle pdb=" N PRO B 986 " pdb=" CA PRO B 986 " pdb=" C PRO B 986 " ideal model delta sigma weight residual 110.70 114.75 -4.05 1.22e+00 6.72e-01 1.10e+01 ... (remaining 46242 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.99: 19371 21.99 - 43.98: 1147 43.98 - 65.96: 156 65.96 - 87.95: 37 87.95 - 109.94: 19 Dihedral angle restraints: 20730 sinusoidal: 8583 harmonic: 12147 Sorted by residual: dihedral pdb=" CB CYS G 23 " pdb=" SG CYS G 23 " pdb=" SG CYS G 88 " pdb=" CB CYS G 88 " ideal model delta sinusoidal sigma weight residual 93.00 -177.22 -89.78 1 1.00e+01 1.00e-02 9.56e+01 dihedral pdb=" CB CYS K 23 " pdb=" SG CYS K 23 " pdb=" SG CYS K 88 " pdb=" CB CYS K 88 " ideal model delta sinusoidal sigma weight residual 93.00 163.29 -70.29 1 1.00e+01 1.00e-02 6.36e+01 dihedral pdb=" CB CYS B 336 " pdb=" SG CYS B 336 " pdb=" SG CYS B 361 " pdb=" CB CYS B 361 " ideal model delta sinusoidal sigma weight residual 93.00 27.56 65.44 1 1.00e+01 1.00e-02 5.61e+01 ... (remaining 20727 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 3727 0.042 - 0.084: 1094 0.084 - 0.126: 424 0.126 - 0.168: 58 0.168 - 0.210: 5 Chirality restraints: 5308 Sorted by residual: chirality pdb=" CA PRO B 809 " pdb=" N PRO B 809 " pdb=" C PRO B 809 " pdb=" CB PRO B 809 " both_signs ideal model delta sigma weight residual False 2.72 2.51 0.21 2.00e-01 2.50e+01 1.11e+00 chirality pdb=" CG LEU A 916 " pdb=" CB LEU A 916 " pdb=" CD1 LEU A 916 " pdb=" CD2 LEU A 916 " both_signs ideal model delta sigma weight residual False -2.59 -2.39 -0.20 2.00e-01 2.50e+01 9.60e-01 chirality pdb=" CA ASP A 614 " pdb=" N ASP A 614 " pdb=" C ASP A 614 " pdb=" CB ASP A 614 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.64e-01 ... (remaining 5305 not shown) Planarity restraints: 5951 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP B 808 " 0.051 5.00e-02 4.00e+02 7.23e-02 8.37e+00 pdb=" N PRO B 809 " -0.125 5.00e-02 4.00e+02 pdb=" CA PRO B 809 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO B 809 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN A 81 " 0.045 5.00e-02 4.00e+02 6.99e-02 7.81e+00 pdb=" N PRO A 82 " -0.121 5.00e-02 4.00e+02 pdb=" CA PRO A 82 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO A 82 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA TYR B 265 " -0.012 2.00e-02 2.50e+03 2.48e-02 6.14e+00 pdb=" C TYR B 265 " 0.043 2.00e-02 2.50e+03 pdb=" O TYR B 265 " -0.016 2.00e-02 2.50e+03 pdb=" N TYR B 266 " -0.014 2.00e-02 2.50e+03 ... (remaining 5948 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 461 2.66 - 3.22: 29475 3.22 - 3.78: 47063 3.78 - 4.34: 65527 4.34 - 4.90: 109965 Nonbonded interactions: 252491 Sorted by model distance: nonbonded pdb=" OH TYR G 36 " pdb=" OE1 GLN G 89 " model vdw 2.099 3.040 nonbonded pdb=" OD1 ASP A 253 " pdb=" OG SER A 256 " model vdw 2.163 3.040 nonbonded pdb=" OD1 ASP B 294 " pdb=" OG1 THR B 632 " model vdw 2.166 3.040 nonbonded pdb=" O ASN C 121 " pdb=" ND2 ASN C 121 " model vdw 2.173 3.120 nonbonded pdb=" NH1 ARG C 246 " pdb=" O SER C 254 " model vdw 2.179 3.120 ... (remaining 252486 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 14 through 1305) selection = (chain 'B' and (resid 14 through 623 or resid 633 through 1305)) selection = (chain 'C' and (resid 14 through 623 or resid 633 through 1305)) } ncs_group { reference = chain 'D' selection = chain 'F' selection = chain 'J' } ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'K' } ncs_group { reference = chain 'I' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 12.760 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.560 Check model and map are aligned: 0.100 Set scattering table: 0.090 Process input model: 29.170 Find NCS groups from input model: 0.800 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:8.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7708 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.147 34089 Z= 0.177 Angle : 0.658 12.089 46473 Z= 0.348 Chirality : 0.046 0.210 5308 Planarity : 0.005 0.072 5918 Dihedral : 13.883 109.939 12794 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.29 % Allowed : 6.89 % Favored : 92.82 % Rotamer: Outliers : 0.03 % Allowed : 0.53 % Favored : 99.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.54 (0.12), residues: 4139 helix: 1.59 (0.22), residues: 636 sheet: -0.46 (0.16), residues: 1032 loop : -2.10 (0.11), residues: 2471 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 102 TYR 0.027 0.001 TYR A 313 PHE 0.030 0.001 PHE C 329 TRP 0.033 0.002 TRP C 886 HIS 0.005 0.001 HIS F 109 Details of bonding type rmsd covalent geometry : bond 0.00387 (33997) covalent geometry : angle 0.64215 (46247) SS BOND : bond 0.00534 ( 50) SS BOND : angle 1.60446 ( 100) hydrogen bonds : bond 0.15069 ( 1043) hydrogen bonds : angle 6.73494 ( 2970) link_BETA1-3 : bond 0.00604 ( 1) link_BETA1-3 : angle 1.96765 ( 3) link_BETA1-4 : bond 0.00509 ( 8) link_BETA1-4 : angle 1.54850 ( 24) link_NAG-ASN : bond 0.00249 ( 33) link_NAG-ASN : angle 2.71142 ( 99) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8278 Ramachandran restraints generated. 4139 Oldfield, 0 Emsley, 4139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8278 Ramachandran restraints generated. 4139 Oldfield, 0 Emsley, 4139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 3617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 197 time to evaluate : 1.211 Fit side-chains revert: symmetry clash REVERT: A 21 ARG cc_start: 0.7144 (mtt180) cc_final: 0.6859 (tpt170) REVERT: A 177 MET cc_start: 0.1430 (ptt) cc_final: 0.0110 (mpp) REVERT: H 2 MET cc_start: 0.0897 (mpp) cc_final: 0.0551 (mpt) outliers start: 1 outliers final: 0 residues processed: 198 average time/residue: 0.6504 time to fit residues: 154.9149 Evaluate side-chains 121 residues out of total 3617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 121 time to evaluate : 1.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 197 optimal weight: 3.9990 chunk 388 optimal weight: 50.0000 chunk 215 optimal weight: 0.9980 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 20.0000 chunk 248 optimal weight: 0.3980 chunk 207 optimal weight: 0.6980 chunk 401 optimal weight: 20.0000 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 3.9990 overall best weight: 2.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 GLN A 185 ASN ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 409 GLN ** A 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 955 ASN B 81 ASN B 501 ASN B 606 ASN B 613 GLN C 957 GLN C1002 GLN ** F 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 39 GLN K 38 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4236 r_free = 0.4236 target = 0.135283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.078268 restraints weight = 87143.813| |-----------------------------------------------------------------------------| r_work (start): 0.3068 rms_B_bonded: 3.96 r_work: 0.2900 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.2900 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2914 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2914 r_free = 0.2914 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2914 r_free = 0.2914 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.2914 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8627 moved from start: 0.0957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 34089 Z= 0.212 Angle : 0.631 11.477 46473 Z= 0.328 Chirality : 0.046 0.225 5308 Planarity : 0.004 0.063 5918 Dihedral : 7.726 81.967 5420 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.27 % Allowed : 6.84 % Favored : 92.90 % Rotamer: Outliers : 0.72 % Allowed : 6.94 % Favored : 92.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.41 (0.12), residues: 4139 helix: 1.86 (0.21), residues: 649 sheet: -0.40 (0.16), residues: 1003 loop : -2.06 (0.11), residues: 2487 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 158 TYR 0.043 0.001 TYR B 265 PHE 0.035 0.002 PHE B 490 TRP 0.015 0.002 TRP B 258 HIS 0.007 0.001 HIS F 35 Details of bonding type rmsd covalent geometry : bond 0.00509 (33997) covalent geometry : angle 0.61705 (46247) SS BOND : bond 0.00607 ( 50) SS BOND : angle 1.53677 ( 100) hydrogen bonds : bond 0.06230 ( 1043) hydrogen bonds : angle 5.48332 ( 2970) link_BETA1-3 : bond 0.00120 ( 1) link_BETA1-3 : angle 1.23249 ( 3) link_BETA1-4 : bond 0.00216 ( 8) link_BETA1-4 : angle 1.24505 ( 24) link_NAG-ASN : bond 0.00323 ( 33) link_NAG-ASN : angle 2.48631 ( 99) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8278 Ramachandran restraints generated. 4139 Oldfield, 0 Emsley, 4139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8278 Ramachandran restraints generated. 4139 Oldfield, 0 Emsley, 4139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 3617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 135 time to evaluate : 1.007 Fit side-chains revert: symmetry clash REVERT: A 21 ARG cc_start: 0.7394 (mtt180) cc_final: 0.6633 (tpt170) REVERT: A 79 PHE cc_start: 0.5135 (p90) cc_final: 0.4534 (p90) REVERT: A 157 PHE cc_start: 0.7011 (t80) cc_final: 0.6615 (t80) REVERT: A 177 MET cc_start: 0.0457 (ptt) cc_final: -0.0141 (mpp) REVERT: A 421 TYR cc_start: 0.7994 (m-80) cc_final: 0.7700 (m-10) REVERT: A 740 MET cc_start: 0.9445 (OUTLIER) cc_final: 0.9076 (ttp) REVERT: B 81 ASN cc_start: 0.8694 (OUTLIER) cc_final: 0.8054 (p0) REVERT: B 329 PHE cc_start: 0.6124 (t80) cc_final: 0.5770 (t80) REVERT: B 740 MET cc_start: 0.9382 (OUTLIER) cc_final: 0.8780 (tmm) REVERT: B 1142 GLN cc_start: 0.8185 (tm-30) cc_final: 0.7904 (tm-30) REVERT: F 51 ILE cc_start: 0.9267 (tp) cc_final: 0.8980 (mp) REVERT: H 2 MET cc_start: 0.1724 (mpp) cc_final: 0.1482 (mpt) REVERT: J 114 MET cc_start: -0.4174 (mmm) cc_final: -0.4941 (mmt) outliers start: 26 outliers final: 11 residues processed: 151 average time/residue: 0.6542 time to fit residues: 120.1155 Evaluate side-chains 136 residues out of total 3617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 122 time to evaluate : 1.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 940 SER Chi-restraints excluded: chain A residue 960 ASN Chi-restraints excluded: chain B residue 81 ASN Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain C residue 538 CYS Chi-restraints excluded: chain D residue 32 TYR Chi-restraints excluded: chain F residue 110 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 96 optimal weight: 0.6980 chunk 250 optimal weight: 6.9990 chunk 295 optimal weight: 6.9990 chunk 333 optimal weight: 50.0000 chunk 308 optimal weight: 2.9990 chunk 251 optimal weight: 9.9990 chunk 129 optimal weight: 0.1980 chunk 92 optimal weight: 2.9990 chunk 179 optimal weight: 2.9990 chunk 289 optimal weight: 2.9990 chunk 291 optimal weight: 0.5980 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 955 ASN C 957 GLN ** F 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4245 r_free = 0.4245 target = 0.139337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.083571 restraints weight = 85594.774| |-----------------------------------------------------------------------------| r_work (start): 0.3104 rms_B_bonded: 4.28 r_work: 0.2913 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2893 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2893 r_free = 0.2893 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2893 r_free = 0.2893 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.2893 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8685 moved from start: 0.1168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 34089 Z= 0.164 Angle : 0.585 10.562 46473 Z= 0.303 Chirality : 0.045 0.198 5308 Planarity : 0.004 0.054 5918 Dihedral : 6.588 61.796 5420 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.26 % Favored : 93.53 % Rotamer: Outliers : 1.13 % Allowed : 8.79 % Favored : 90.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.29 (0.13), residues: 4139 helix: 2.00 (0.21), residues: 655 sheet: -0.33 (0.16), residues: 1032 loop : -2.02 (0.11), residues: 2452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 403 TYR 0.037 0.001 TYR B 265 PHE 0.022 0.001 PHE B 329 TRP 0.012 0.001 TRP C 886 HIS 0.005 0.001 HIS F 35 Details of bonding type rmsd covalent geometry : bond 0.00390 (33997) covalent geometry : angle 0.57093 (46247) SS BOND : bond 0.00466 ( 50) SS BOND : angle 1.37797 ( 100) hydrogen bonds : bond 0.05739 ( 1043) hydrogen bonds : angle 5.23700 ( 2970) link_BETA1-3 : bond 0.00710 ( 1) link_BETA1-3 : angle 1.35093 ( 3) link_BETA1-4 : bond 0.00203 ( 8) link_BETA1-4 : angle 1.33341 ( 24) link_NAG-ASN : bond 0.00267 ( 33) link_NAG-ASN : angle 2.39465 ( 99) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8278 Ramachandran restraints generated. 4139 Oldfield, 0 Emsley, 4139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8278 Ramachandran restraints generated. 4139 Oldfield, 0 Emsley, 4139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 3617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 131 time to evaluate : 1.193 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 21 ARG cc_start: 0.7296 (mtt180) cc_final: 0.6598 (tpt170) REVERT: A 79 PHE cc_start: 0.5188 (p90) cc_final: 0.4264 (p90) REVERT: A 157 PHE cc_start: 0.7171 (t80) cc_final: 0.6716 (t80) REVERT: A 177 MET cc_start: 0.0730 (ptt) cc_final: -0.0413 (mpp) REVERT: A 740 MET cc_start: 0.9472 (OUTLIER) cc_final: 0.9104 (ttp) REVERT: B 329 PHE cc_start: 0.6256 (t80) cc_final: 0.5983 (t80) REVERT: B 395 VAL cc_start: 0.6749 (t) cc_final: 0.6476 (m) REVERT: B 501 ASN cc_start: 0.7933 (OUTLIER) cc_final: 0.7707 (m-40) REVERT: B 740 MET cc_start: 0.9409 (OUTLIER) cc_final: 0.8775 (tmm) REVERT: B 994 ASP cc_start: 0.9059 (OUTLIER) cc_final: 0.8680 (t0) REVERT: B 1142 GLN cc_start: 0.8288 (tm-30) cc_final: 0.7944 (tm-30) REVERT: C 396 TYR cc_start: 0.6879 (m-10) cc_final: 0.6630 (m-10) REVERT: F 51 ILE cc_start: 0.9328 (tp) cc_final: 0.9078 (mp) REVERT: J 114 MET cc_start: -0.5134 (mmm) cc_final: -0.5553 (mmt) outliers start: 41 outliers final: 16 residues processed: 162 average time/residue: 0.6641 time to fit residues: 130.5900 Evaluate side-chains 146 residues out of total 3617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 126 time to evaluate : 1.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 960 ASN Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 421 TYR Chi-restraints excluded: chain B residue 501 ASN Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 895 GLN Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1076 THR Chi-restraints excluded: chain C residue 538 CYS Chi-restraints excluded: chain D residue 32 TYR Chi-restraints excluded: chain F residue 110 TYR Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain K residue 12 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 71 optimal weight: 2.9990 chunk 127 optimal weight: 2.9990 chunk 327 optimal weight: 20.0000 chunk 166 optimal weight: 2.9990 chunk 249 optimal weight: 9.9990 chunk 348 optimal weight: 4.9990 chunk 363 optimal weight: 20.0000 chunk 272 optimal weight: 3.9990 chunk 380 optimal weight: 20.0000 chunk 391 optimal weight: 0.0970 chunk 242 optimal weight: 1.9990 overall best weight: 2.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN A 239 GLN ** A 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 955 ASN A1002 GLN B 81 ASN B 607 GLN C 957 GLN ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4228 r_free = 0.4228 target = 0.138150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.082279 restraints weight = 85211.892| |-----------------------------------------------------------------------------| r_work (start): 0.3075 rms_B_bonded: 4.38 r_work: 0.2874 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.2874 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2857 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2857 r_free = 0.2857 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2857 r_free = 0.2857 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.2857 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8693 moved from start: 0.1437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.085 34089 Z= 0.225 Angle : 0.618 8.768 46473 Z= 0.320 Chirality : 0.046 0.174 5308 Planarity : 0.004 0.052 5918 Dihedral : 6.127 59.889 5420 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.98 % Favored : 92.78 % Rotamer: Outliers : 1.44 % Allowed : 10.32 % Favored : 88.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.35 (0.13), residues: 4139 helix: 2.06 (0.21), residues: 651 sheet: -0.42 (0.16), residues: 1009 loop : -2.04 (0.11), residues: 2479 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 403 TYR 0.048 0.001 TYR B 265 PHE 0.037 0.002 PHE B 490 TRP 0.015 0.001 TRP C 886 HIS 0.006 0.001 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00542 (33997) covalent geometry : angle 0.60403 (46247) SS BOND : bond 0.00566 ( 50) SS BOND : angle 1.62672 ( 100) hydrogen bonds : bond 0.06311 ( 1043) hydrogen bonds : angle 5.22376 ( 2970) link_BETA1-3 : bond 0.00117 ( 1) link_BETA1-3 : angle 1.19610 ( 3) link_BETA1-4 : bond 0.00294 ( 8) link_BETA1-4 : angle 1.41303 ( 24) link_NAG-ASN : bond 0.00324 ( 33) link_NAG-ASN : angle 2.43255 ( 99) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8278 Ramachandran restraints generated. 4139 Oldfield, 0 Emsley, 4139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8278 Ramachandran restraints generated. 4139 Oldfield, 0 Emsley, 4139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 3617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 133 time to evaluate : 1.093 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 21 ARG cc_start: 0.7322 (mtt180) cc_final: 0.6675 (tpt170) REVERT: A 79 PHE cc_start: 0.5222 (p90) cc_final: 0.4488 (p90) REVERT: A 177 MET cc_start: 0.0706 (ptt) cc_final: -0.0526 (mpp) REVERT: A 421 TYR cc_start: 0.8108 (m-80) cc_final: 0.7870 (m-80) REVERT: B 79 PHE cc_start: 0.7099 (t80) cc_final: 0.6714 (t80) REVERT: B 395 VAL cc_start: 0.6784 (t) cc_final: 0.6476 (m) REVERT: B 740 MET cc_start: 0.9411 (OUTLIER) cc_final: 0.8805 (tmm) REVERT: B 994 ASP cc_start: 0.9138 (OUTLIER) cc_final: 0.8742 (t0) REVERT: B 1142 GLN cc_start: 0.8329 (tm-30) cc_final: 0.8080 (tm-30) REVERT: F 51 ILE cc_start: 0.9270 (OUTLIER) cc_final: 0.9012 (mp) REVERT: J 114 MET cc_start: -0.4924 (mmm) cc_final: -0.5416 (mmt) outliers start: 52 outliers final: 22 residues processed: 175 average time/residue: 0.5445 time to fit residues: 117.9023 Evaluate side-chains 144 residues out of total 3617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 119 time to evaluate : 1.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 960 ASN Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 421 TYR Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 501 ASN Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 895 GLN Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1076 THR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 538 CYS Chi-restraints excluded: chain D residue 32 TYR Chi-restraints excluded: chain F residue 51 ILE Chi-restraints excluded: chain F residue 110 TYR Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain J residue 11 VAL Chi-restraints excluded: chain K residue 12 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 23 optimal weight: 0.0870 chunk 274 optimal weight: 0.9990 chunk 20 optimal weight: 4.9990 chunk 222 optimal weight: 4.9990 chunk 174 optimal weight: 3.9990 chunk 122 optimal weight: 7.9990 chunk 28 optimal weight: 2.9990 chunk 219 optimal weight: 1.9990 chunk 366 optimal weight: 3.9990 chunk 284 optimal weight: 1.9990 chunk 158 optimal weight: 0.6980 overall best weight: 1.1564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 360 ASN ** A 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 955 ASN A1002 GLN B 146 HIS C 957 GLN E 38 GLN ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.139242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.082060 restraints weight = 85016.011| |-----------------------------------------------------------------------------| r_work (start): 0.3102 rms_B_bonded: 3.48 r_work: 0.2937 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2928 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2928 r_free = 0.2928 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2928 r_free = 0.2928 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.2928 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8627 moved from start: 0.1545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 34089 Z= 0.139 Angle : 0.568 7.886 46473 Z= 0.293 Chirality : 0.044 0.179 5308 Planarity : 0.004 0.051 5918 Dihedral : 5.733 58.304 5420 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.16 % Favored : 93.62 % Rotamer: Outliers : 1.44 % Allowed : 11.56 % Favored : 87.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.20 (0.13), residues: 4139 helix: 2.18 (0.21), residues: 655 sheet: -0.32 (0.16), residues: 1003 loop : -1.95 (0.11), residues: 2481 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 237 TYR 0.032 0.001 TYR B 265 PHE 0.022 0.001 PHE B 329 TRP 0.015 0.001 TRP F 47 HIS 0.003 0.001 HIS J 35 Details of bonding type rmsd covalent geometry : bond 0.00326 (33997) covalent geometry : angle 0.55522 (46247) SS BOND : bond 0.00405 ( 50) SS BOND : angle 1.42758 ( 100) hydrogen bonds : bond 0.05340 ( 1043) hydrogen bonds : angle 5.00228 ( 2970) link_BETA1-3 : bond 0.00536 ( 1) link_BETA1-3 : angle 1.25439 ( 3) link_BETA1-4 : bond 0.00345 ( 8) link_BETA1-4 : angle 1.43416 ( 24) link_NAG-ASN : bond 0.00232 ( 33) link_NAG-ASN : angle 2.22011 ( 99) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8278 Ramachandran restraints generated. 4139 Oldfield, 0 Emsley, 4139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8278 Ramachandran restraints generated. 4139 Oldfield, 0 Emsley, 4139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 3617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 128 time to evaluate : 1.216 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 21 ARG cc_start: 0.7383 (mtt180) cc_final: 0.6731 (tpt170) REVERT: A 79 PHE cc_start: 0.5336 (p90) cc_final: 0.4468 (p90) REVERT: A 177 MET cc_start: 0.0741 (ptt) cc_final: -0.0526 (mpp) REVERT: A 421 TYR cc_start: 0.8029 (m-80) cc_final: 0.7802 (m-80) REVERT: A 740 MET cc_start: 0.9441 (OUTLIER) cc_final: 0.9050 (ttp) REVERT: B 79 PHE cc_start: 0.7058 (t80) cc_final: 0.6737 (t80) REVERT: B 395 VAL cc_start: 0.6730 (t) cc_final: 0.6486 (m) REVERT: B 448 ASN cc_start: 0.3184 (OUTLIER) cc_final: 0.2900 (p0) REVERT: B 493 GLN cc_start: 0.8606 (OUTLIER) cc_final: 0.7961 (tt0) REVERT: B 495 TYR cc_start: 0.3234 (t80) cc_final: 0.2880 (t80) REVERT: B 740 MET cc_start: 0.9385 (OUTLIER) cc_final: 0.8700 (tmm) REVERT: B 994 ASP cc_start: 0.8996 (OUTLIER) cc_final: 0.8686 (t0) REVERT: B 1142 GLN cc_start: 0.8343 (tm-30) cc_final: 0.8072 (tm-30) REVERT: F 51 ILE cc_start: 0.9306 (OUTLIER) cc_final: 0.9000 (mp) REVERT: G 4 MET cc_start: 0.6976 (mmm) cc_final: 0.6087 (mmm) REVERT: J 114 MET cc_start: -0.4427 (mmm) cc_final: -0.5048 (mmt) REVERT: K 23 CYS cc_start: 0.6340 (OUTLIER) cc_final: 0.3934 (m) outliers start: 52 outliers final: 25 residues processed: 172 average time/residue: 0.6186 time to fit residues: 131.4889 Evaluate side-chains 150 residues out of total 3617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 118 time to evaluate : 1.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 421 TYR Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 448 ASN Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 493 GLN Chi-restraints excluded: chain B residue 501 ASN Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 696 THR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 895 GLN Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1076 THR Chi-restraints excluded: chain C residue 538 CYS Chi-restraints excluded: chain D residue 32 TYR Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain F residue 51 ILE Chi-restraints excluded: chain F residue 110 TYR Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain K residue 12 SER Chi-restraints excluded: chain K residue 23 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 156 optimal weight: 8.9990 chunk 185 optimal weight: 1.9990 chunk 143 optimal weight: 0.0170 chunk 285 optimal weight: 0.9990 chunk 172 optimal weight: 0.9980 chunk 168 optimal weight: 4.9990 chunk 345 optimal weight: 10.0000 chunk 379 optimal weight: 0.7980 chunk 318 optimal weight: 1.9990 chunk 37 optimal weight: 10.0000 chunk 159 optimal weight: 0.9980 overall best weight: 0.7620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 HIS A 360 ASN ** A 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1002 GLN B 360 ASN C 957 GLN ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4250 r_free = 0.4250 target = 0.139841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.082952 restraints weight = 85015.228| |-----------------------------------------------------------------------------| r_work (start): 0.3123 rms_B_bonded: 3.42 r_work: 0.2960 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2944 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2944 r_free = 0.2944 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2944 r_free = 0.2944 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.2944 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8611 moved from start: 0.1700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 34089 Z= 0.114 Angle : 0.547 9.053 46473 Z= 0.281 Chirality : 0.043 0.181 5308 Planarity : 0.004 0.056 5918 Dihedral : 5.435 56.323 5420 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.02 % Favored : 93.77 % Rotamer: Outliers : 1.49 % Allowed : 12.53 % Favored : 85.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.05 (0.13), residues: 4139 helix: 2.34 (0.21), residues: 655 sheet: -0.16 (0.17), residues: 974 loop : -1.88 (0.11), residues: 2510 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 403 TYR 0.025 0.001 TYR B 265 PHE 0.040 0.001 PHE B 490 TRP 0.023 0.001 TRP F 47 HIS 0.003 0.001 HIS J 35 Details of bonding type rmsd covalent geometry : bond 0.00259 (33997) covalent geometry : angle 0.53576 (46247) SS BOND : bond 0.00359 ( 50) SS BOND : angle 1.29143 ( 100) hydrogen bonds : bond 0.04764 ( 1043) hydrogen bonds : angle 4.81034 ( 2970) link_BETA1-3 : bond 0.00757 ( 1) link_BETA1-3 : angle 1.35355 ( 3) link_BETA1-4 : bond 0.00412 ( 8) link_BETA1-4 : angle 1.39753 ( 24) link_NAG-ASN : bond 0.00224 ( 33) link_NAG-ASN : angle 2.06374 ( 99) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8278 Ramachandran restraints generated. 4139 Oldfield, 0 Emsley, 4139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8278 Ramachandran restraints generated. 4139 Oldfield, 0 Emsley, 4139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 3617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 126 time to evaluate : 1.317 Fit side-chains revert: symmetry clash REVERT: A 21 ARG cc_start: 0.7426 (mtt180) cc_final: 0.6734 (tpt170) REVERT: A 79 PHE cc_start: 0.5595 (p90) cc_final: 0.4645 (p90) REVERT: A 177 MET cc_start: 0.0581 (ptt) cc_final: -0.0697 (mpp) REVERT: A 421 TYR cc_start: 0.8129 (m-80) cc_final: 0.7920 (m-80) REVERT: A 740 MET cc_start: 0.9414 (OUTLIER) cc_final: 0.9014 (ttp) REVERT: B 79 PHE cc_start: 0.6822 (t80) cc_final: 0.6005 (p90) REVERT: B 190 ARG cc_start: 0.7979 (ttm170) cc_final: 0.7698 (mtt-85) REVERT: B 493 GLN cc_start: 0.8597 (OUTLIER) cc_final: 0.7934 (tt0) REVERT: B 553 THR cc_start: 0.8535 (OUTLIER) cc_final: 0.8211 (m) REVERT: B 740 MET cc_start: 0.9385 (OUTLIER) cc_final: 0.8679 (tmm) REVERT: B 1142 GLN cc_start: 0.8271 (tm-30) cc_final: 0.8018 (tm-30) REVERT: C 133 PHE cc_start: 0.8131 (OUTLIER) cc_final: 0.6717 (p90) REVERT: C 144 TYR cc_start: 0.6758 (t80) cc_final: 0.6234 (t80) REVERT: C 624 ILE cc_start: 0.6279 (OUTLIER) cc_final: 0.6024 (mm) REVERT: F 51 ILE cc_start: 0.9278 (OUTLIER) cc_final: 0.8979 (mp) REVERT: G 4 MET cc_start: 0.6948 (mmm) cc_final: 0.6070 (mmm) REVERT: J 114 MET cc_start: -0.4761 (mmm) cc_final: -0.5298 (mmt) REVERT: K 12 SER cc_start: 0.3354 (OUTLIER) cc_final: 0.3106 (m) REVERT: K 23 CYS cc_start: 0.6493 (OUTLIER) cc_final: 0.4222 (m) outliers start: 54 outliers final: 28 residues processed: 170 average time/residue: 0.6271 time to fit residues: 131.1846 Evaluate side-chains 158 residues out of total 3617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 121 time to evaluate : 1.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 421 TYR Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 493 GLN Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 696 THR Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 133 PHE Chi-restraints excluded: chain C residue 538 CYS Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 624 ILE Chi-restraints excluded: chain D residue 32 TYR Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain F residue 51 ILE Chi-restraints excluded: chain F residue 60 TYR Chi-restraints excluded: chain F residue 110 TYR Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain J residue 11 VAL Chi-restraints excluded: chain K residue 12 SER Chi-restraints excluded: chain K residue 23 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 384 optimal weight: 30.0000 chunk 301 optimal weight: 2.9990 chunk 293 optimal weight: 0.6980 chunk 75 optimal weight: 1.9990 chunk 304 optimal weight: 3.9990 chunk 163 optimal weight: 5.9990 chunk 273 optimal weight: 3.9990 chunk 179 optimal weight: 3.9990 chunk 352 optimal weight: 0.9990 chunk 272 optimal weight: 1.9990 chunk 191 optimal weight: 0.9980 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 360 ASN ** A 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.139100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.081975 restraints weight = 85398.460| |-----------------------------------------------------------------------------| r_work (start): 0.3109 rms_B_bonded: 3.48 r_work: 0.2953 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2939 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2939 r_free = 0.2939 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2939 r_free = 0.2939 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.2939 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8574 moved from start: 0.1771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 34089 Z= 0.151 Angle : 0.560 9.056 46473 Z= 0.288 Chirality : 0.044 0.170 5308 Planarity : 0.004 0.058 5918 Dihedral : 5.448 57.998 5420 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.28 % Favored : 93.53 % Rotamer: Outliers : 1.63 % Allowed : 13.33 % Favored : 85.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.05 (0.13), residues: 4139 helix: 2.31 (0.21), residues: 656 sheet: -0.16 (0.17), residues: 970 loop : -1.87 (0.11), residues: 2513 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 24 TYR 0.034 0.001 TYR B 265 PHE 0.015 0.001 PHE C 329 TRP 0.018 0.001 TRP F 47 HIS 0.004 0.001 HIS F 109 Details of bonding type rmsd covalent geometry : bond 0.00359 (33997) covalent geometry : angle 0.54813 (46247) SS BOND : bond 0.00446 ( 50) SS BOND : angle 1.37458 ( 100) hydrogen bonds : bond 0.05247 ( 1043) hydrogen bonds : angle 4.85452 ( 2970) link_BETA1-3 : bond 0.00487 ( 1) link_BETA1-3 : angle 1.21879 ( 3) link_BETA1-4 : bond 0.00324 ( 8) link_BETA1-4 : angle 1.38497 ( 24) link_NAG-ASN : bond 0.00232 ( 33) link_NAG-ASN : angle 2.06849 ( 99) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8278 Ramachandran restraints generated. 4139 Oldfield, 0 Emsley, 4139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8278 Ramachandran restraints generated. 4139 Oldfield, 0 Emsley, 4139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 3617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 121 time to evaluate : 1.282 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 21 ARG cc_start: 0.7382 (mtt180) cc_final: 0.6712 (tpt170) REVERT: A 79 PHE cc_start: 0.5563 (p90) cc_final: 0.4538 (p90) REVERT: A 177 MET cc_start: 0.0522 (ptt) cc_final: -0.0575 (mpp) REVERT: A 421 TYR cc_start: 0.8130 (m-80) cc_final: 0.7920 (m-80) REVERT: B 79 PHE cc_start: 0.6840 (t80) cc_final: 0.6544 (t80) REVERT: B 190 ARG cc_start: 0.7915 (ttm170) cc_final: 0.7621 (mtt-85) REVERT: B 493 GLN cc_start: 0.8674 (OUTLIER) cc_final: 0.8010 (tt0) REVERT: B 740 MET cc_start: 0.9381 (OUTLIER) cc_final: 0.8694 (tmm) REVERT: B 1142 GLN cc_start: 0.8285 (tm-30) cc_final: 0.8017 (tm-30) REVERT: C 133 PHE cc_start: 0.8154 (OUTLIER) cc_final: 0.6761 (p90) REVERT: C 144 TYR cc_start: 0.6787 (t80) cc_final: 0.6265 (t80) REVERT: C 624 ILE cc_start: 0.6203 (OUTLIER) cc_final: 0.5991 (mm) REVERT: F 51 ILE cc_start: 0.9282 (OUTLIER) cc_final: 0.8992 (mp) REVERT: G 27 GLN cc_start: 0.7195 (pt0) cc_final: 0.6840 (pp30) REVERT: J 114 MET cc_start: -0.4332 (mmm) cc_final: -0.5019 (mmt) REVERT: K 12 SER cc_start: 0.3435 (OUTLIER) cc_final: 0.3154 (m) REVERT: K 23 CYS cc_start: 0.5622 (OUTLIER) cc_final: 0.2640 (m) outliers start: 59 outliers final: 32 residues processed: 170 average time/residue: 0.6342 time to fit residues: 133.2083 Evaluate side-chains 156 residues out of total 3617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 117 time to evaluate : 1.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 421 TYR Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 493 GLN Chi-restraints excluded: chain B residue 501 ASN Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 696 THR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 1076 THR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 133 PHE Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 538 CYS Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 624 ILE Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain D residue 32 TYR Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain F residue 51 ILE Chi-restraints excluded: chain F residue 60 TYR Chi-restraints excluded: chain F residue 110 TYR Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain J residue 11 VAL Chi-restraints excluded: chain K residue 12 SER Chi-restraints excluded: chain K residue 23 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 403 optimal weight: 50.0000 chunk 111 optimal weight: 1.9990 chunk 222 optimal weight: 4.9990 chunk 113 optimal weight: 0.7980 chunk 32 optimal weight: 0.0010 chunk 7 optimal weight: 7.9990 chunk 368 optimal weight: 0.5980 chunk 162 optimal weight: 3.9990 chunk 121 optimal weight: 4.9990 chunk 223 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 overall best weight: 1.0790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 121 ASN ** C 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.139495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.082457 restraints weight = 84808.604| |-----------------------------------------------------------------------------| r_work (start): 0.3115 rms_B_bonded: 3.40 r_work: 0.2952 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2927 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2927 r_free = 0.2927 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2927 r_free = 0.2927 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.2927 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8674 moved from start: 0.1855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 34089 Z= 0.130 Angle : 0.556 8.957 46473 Z= 0.285 Chirality : 0.043 0.230 5308 Planarity : 0.004 0.059 5918 Dihedral : 5.394 59.374 5420 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.02 % Favored : 93.79 % Rotamer: Outliers : 1.52 % Allowed : 13.83 % Favored : 84.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.00 (0.13), residues: 4139 helix: 2.34 (0.21), residues: 656 sheet: -0.15 (0.17), residues: 989 loop : -1.83 (0.11), residues: 2494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 24 TYR 0.029 0.001 TYR B 265 PHE 0.040 0.001 PHE B 490 TRP 0.018 0.001 TRP F 47 HIS 0.003 0.001 HIS J 35 Details of bonding type rmsd covalent geometry : bond 0.00306 (33997) covalent geometry : angle 0.54406 (46247) SS BOND : bond 0.00383 ( 50) SS BOND : angle 1.34209 ( 100) hydrogen bonds : bond 0.05023 ( 1043) hydrogen bonds : angle 4.79572 ( 2970) link_BETA1-3 : bond 0.00512 ( 1) link_BETA1-3 : angle 1.22485 ( 3) link_BETA1-4 : bond 0.00353 ( 8) link_BETA1-4 : angle 1.37750 ( 24) link_NAG-ASN : bond 0.00212 ( 33) link_NAG-ASN : angle 2.07802 ( 99) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8278 Ramachandran restraints generated. 4139 Oldfield, 0 Emsley, 4139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8278 Ramachandran restraints generated. 4139 Oldfield, 0 Emsley, 4139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 3617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 121 time to evaluate : 1.289 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 21 ARG cc_start: 0.7405 (mtt180) cc_final: 0.6705 (tpt170) REVERT: A 79 PHE cc_start: 0.5639 (p90) cc_final: 0.4713 (p90) REVERT: A 177 MET cc_start: 0.0784 (ptt) cc_final: -0.0473 (mpp) REVERT: A 324 GLU cc_start: 0.8936 (OUTLIER) cc_final: 0.8379 (pm20) REVERT: A 421 TYR cc_start: 0.8185 (m-80) cc_final: 0.7954 (m-10) REVERT: B 79 PHE cc_start: 0.6772 (t80) cc_final: 0.6518 (t80) REVERT: B 190 ARG cc_start: 0.7894 (ttm170) cc_final: 0.7580 (mtt-85) REVERT: B 493 GLN cc_start: 0.8646 (OUTLIER) cc_final: 0.7993 (tt0) REVERT: B 740 MET cc_start: 0.9378 (OUTLIER) cc_final: 0.8678 (tmm) REVERT: B 1142 GLN cc_start: 0.8302 (tm-30) cc_final: 0.8030 (tm-30) REVERT: C 144 TYR cc_start: 0.6846 (t80) cc_final: 0.6310 (t80) REVERT: C 624 ILE cc_start: 0.6165 (OUTLIER) cc_final: 0.5954 (mm) REVERT: F 51 ILE cc_start: 0.9205 (OUTLIER) cc_final: 0.8951 (mp) REVERT: G 24 ARG cc_start: 0.8029 (ttp-110) cc_final: 0.7554 (tmm-80) REVERT: G 27 GLN cc_start: 0.6808 (pt0) cc_final: 0.6542 (pp30) REVERT: J 114 MET cc_start: -0.5248 (mmm) cc_final: -0.5544 (mmt) REVERT: K 23 CYS cc_start: 0.7819 (OUTLIER) cc_final: 0.6655 (m) outliers start: 55 outliers final: 35 residues processed: 166 average time/residue: 0.6074 time to fit residues: 124.2862 Evaluate side-chains 158 residues out of total 3617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 117 time to evaluate : 1.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 421 TYR Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 493 GLN Chi-restraints excluded: chain B residue 501 ASN Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 696 THR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 895 GLN Chi-restraints excluded: chain B residue 1076 THR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 538 CYS Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 624 ILE Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain D residue 32 TYR Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain F residue 51 ILE Chi-restraints excluded: chain F residue 60 TYR Chi-restraints excluded: chain F residue 110 TYR Chi-restraints excluded: chain H residue 2 MET Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain J residue 11 VAL Chi-restraints excluded: chain K residue 20 ILE Chi-restraints excluded: chain K residue 23 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 363 optimal weight: 20.0000 chunk 218 optimal weight: 0.9990 chunk 226 optimal weight: 4.9990 chunk 278 optimal weight: 1.9990 chunk 175 optimal weight: 0.7980 chunk 170 optimal weight: 0.9980 chunk 372 optimal weight: 40.0000 chunk 41 optimal weight: 1.9990 chunk 224 optimal weight: 3.9990 chunk 67 optimal weight: 0.5980 chunk 312 optimal weight: 2.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 6 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4245 r_free = 0.4245 target = 0.139368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.082494 restraints weight = 84526.423| |-----------------------------------------------------------------------------| r_work (start): 0.3124 rms_B_bonded: 3.44 r_work: 0.2956 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2928 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2928 r_free = 0.2928 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2928 r_free = 0.2928 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.2928 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8671 moved from start: 0.1939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 34089 Z= 0.130 Angle : 0.554 9.854 46473 Z= 0.283 Chirality : 0.043 0.223 5308 Planarity : 0.004 0.059 5918 Dihedral : 5.301 57.529 5420 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.11 % Favored : 93.69 % Rotamer: Outliers : 1.36 % Allowed : 14.13 % Favored : 84.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.97 (0.13), residues: 4139 helix: 2.36 (0.21), residues: 656 sheet: -0.10 (0.17), residues: 982 loop : -1.82 (0.11), residues: 2501 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 403 TYR 0.029 0.001 TYR B 265 PHE 0.015 0.001 PHE C 329 TRP 0.023 0.001 TRP F 47 HIS 0.004 0.001 HIS F 109 Details of bonding type rmsd covalent geometry : bond 0.00306 (33997) covalent geometry : angle 0.54291 (46247) SS BOND : bond 0.00386 ( 50) SS BOND : angle 1.30310 ( 100) hydrogen bonds : bond 0.04984 ( 1043) hydrogen bonds : angle 4.74356 ( 2970) link_BETA1-3 : bond 0.00485 ( 1) link_BETA1-3 : angle 1.22491 ( 3) link_BETA1-4 : bond 0.00343 ( 8) link_BETA1-4 : angle 1.36202 ( 24) link_NAG-ASN : bond 0.00205 ( 33) link_NAG-ASN : angle 2.03030 ( 99) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8278 Ramachandran restraints generated. 4139 Oldfield, 0 Emsley, 4139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8278 Ramachandran restraints generated. 4139 Oldfield, 0 Emsley, 4139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 3617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 124 time to evaluate : 1.424 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 21 ARG cc_start: 0.7429 (mtt180) cc_final: 0.6740 (tpt170) REVERT: A 79 PHE cc_start: 0.5586 (p90) cc_final: 0.4904 (p90) REVERT: A 177 MET cc_start: 0.0903 (ptt) cc_final: -0.0393 (mpp) REVERT: A 258 TRP cc_start: 0.5832 (p-90) cc_final: 0.3954 (p90) REVERT: A 324 GLU cc_start: 0.8953 (OUTLIER) cc_final: 0.8403 (pm20) REVERT: A 421 TYR cc_start: 0.8223 (m-80) cc_final: 0.7972 (m-10) REVERT: A 960 ASN cc_start: 0.9024 (OUTLIER) cc_final: 0.8751 (t0) REVERT: B 79 PHE cc_start: 0.6794 (t80) cc_final: 0.6554 (t80) REVERT: B 190 ARG cc_start: 0.7949 (ttm170) cc_final: 0.7624 (mtt-85) REVERT: B 493 GLN cc_start: 0.8643 (OUTLIER) cc_final: 0.7994 (tt0) REVERT: B 740 MET cc_start: 0.9383 (OUTLIER) cc_final: 0.8693 (tmm) REVERT: B 1142 GLN cc_start: 0.8334 (tm-30) cc_final: 0.8053 (tm-30) REVERT: C 133 PHE cc_start: 0.8143 (OUTLIER) cc_final: 0.6840 (p90) REVERT: C 144 TYR cc_start: 0.6915 (t80) cc_final: 0.6379 (t80) REVERT: C 624 ILE cc_start: 0.6258 (OUTLIER) cc_final: 0.6041 (mm) REVERT: F 51 ILE cc_start: 0.9219 (OUTLIER) cc_final: 0.8933 (mp) REVERT: G 24 ARG cc_start: 0.8067 (ttp-110) cc_final: 0.7560 (tmm-80) REVERT: G 27 GLN cc_start: 0.7028 (pt0) cc_final: 0.6736 (pp30) REVERT: J 114 MET cc_start: -0.5155 (mmm) cc_final: -0.5491 (mmt) REVERT: K 23 CYS cc_start: 0.7694 (OUTLIER) cc_final: 0.6364 (m) outliers start: 49 outliers final: 35 residues processed: 164 average time/residue: 0.6426 time to fit residues: 128.9491 Evaluate side-chains 163 residues out of total 3617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 120 time to evaluate : 1.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 960 ASN Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 421 TYR Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 493 GLN Chi-restraints excluded: chain B residue 501 ASN Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 696 THR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 895 GLN Chi-restraints excluded: chain B residue 1076 THR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 133 PHE Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 538 CYS Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 624 ILE Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain D residue 32 TYR Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain F residue 51 ILE Chi-restraints excluded: chain F residue 60 TYR Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain J residue 11 VAL Chi-restraints excluded: chain K residue 20 ILE Chi-restraints excluded: chain K residue 23 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 1 optimal weight: 5.9990 chunk 257 optimal weight: 8.9990 chunk 54 optimal weight: 0.6980 chunk 290 optimal weight: 1.9990 chunk 374 optimal weight: 1.9990 chunk 333 optimal weight: 50.0000 chunk 2 optimal weight: 0.3980 chunk 242 optimal weight: 0.0770 chunk 303 optimal weight: 2.9990 chunk 404 optimal weight: 10.0000 chunk 389 optimal weight: 8.9990 overall best weight: 1.0342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 115 GLN ** C 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 79 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4247 r_free = 0.4247 target = 0.139455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.082475 restraints weight = 85570.528| |-----------------------------------------------------------------------------| r_work (start): 0.3114 rms_B_bonded: 3.43 r_work: 0.2949 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2935 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2935 r_free = 0.2935 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2935 r_free = 0.2935 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.2935 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8638 moved from start: 0.2006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 34089 Z= 0.128 Angle : 0.559 12.069 46473 Z= 0.285 Chirality : 0.043 0.196 5308 Planarity : 0.004 0.058 5918 Dihedral : 5.229 57.494 5420 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.06 % Favored : 93.77 % Rotamer: Outliers : 1.33 % Allowed : 14.24 % Favored : 84.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.95 (0.13), residues: 4139 helix: 2.38 (0.21), residues: 656 sheet: -0.10 (0.17), residues: 987 loop : -1.79 (0.11), residues: 2496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 403 TYR 0.028 0.001 TYR B 265 PHE 0.042 0.001 PHE B 490 TRP 0.019 0.001 TRP F 47 HIS 0.011 0.001 HIS F 35 Details of bonding type rmsd covalent geometry : bond 0.00300 (33997) covalent geometry : angle 0.54790 (46247) SS BOND : bond 0.00376 ( 50) SS BOND : angle 1.30673 ( 100) hydrogen bonds : bond 0.04908 ( 1043) hydrogen bonds : angle 4.71583 ( 2970) link_BETA1-3 : bond 0.00515 ( 1) link_BETA1-3 : angle 1.23435 ( 3) link_BETA1-4 : bond 0.00362 ( 8) link_BETA1-4 : angle 1.34722 ( 24) link_NAG-ASN : bond 0.00198 ( 33) link_NAG-ASN : angle 2.03106 ( 99) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8278 Ramachandran restraints generated. 4139 Oldfield, 0 Emsley, 4139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8278 Ramachandran restraints generated. 4139 Oldfield, 0 Emsley, 4139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 3617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 119 time to evaluate : 1.320 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 21 ARG cc_start: 0.7406 (mtt180) cc_final: 0.6691 (tpt170) REVERT: A 79 PHE cc_start: 0.5570 (p90) cc_final: 0.4632 (p90) REVERT: A 177 MET cc_start: 0.0846 (ptt) cc_final: -0.0517 (mpp) REVERT: A 324 GLU cc_start: 0.8993 (OUTLIER) cc_final: 0.8432 (pm20) REVERT: A 421 TYR cc_start: 0.8189 (m-80) cc_final: 0.7938 (m-10) REVERT: A 960 ASN cc_start: 0.9042 (OUTLIER) cc_final: 0.8771 (t0) REVERT: B 79 PHE cc_start: 0.6795 (t80) cc_final: 0.5798 (p90) REVERT: B 190 ARG cc_start: 0.7983 (ttm170) cc_final: 0.7660 (mtt-85) REVERT: B 493 GLN cc_start: 0.8606 (OUTLIER) cc_final: 0.7935 (tt0) REVERT: B 740 MET cc_start: 0.9381 (OUTLIER) cc_final: 0.8685 (tmm) REVERT: B 1142 GLN cc_start: 0.8273 (tm-30) cc_final: 0.8006 (tm-30) REVERT: C 133 PHE cc_start: 0.8168 (OUTLIER) cc_final: 0.6832 (p90) REVERT: C 144 TYR cc_start: 0.6929 (t80) cc_final: 0.6407 (t80) REVERT: F 51 ILE cc_start: 0.9153 (OUTLIER) cc_final: 0.8873 (mp) REVERT: G 24 ARG cc_start: 0.8097 (ttp-110) cc_final: 0.7588 (tmm-80) REVERT: J 114 MET cc_start: -0.4873 (mmm) cc_final: -0.5312 (mmt) REVERT: K 23 CYS cc_start: 0.7026 (OUTLIER) cc_final: 0.4838 (m) outliers start: 48 outliers final: 37 residues processed: 159 average time/residue: 0.6040 time to fit residues: 118.0944 Evaluate side-chains 161 residues out of total 3617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 117 time to evaluate : 1.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 960 ASN Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 421 TYR Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 493 GLN Chi-restraints excluded: chain B residue 501 ASN Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 696 THR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 895 GLN Chi-restraints excluded: chain B residue 1076 THR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 133 PHE Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 538 CYS Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain D residue 32 TYR Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain F residue 51 ILE Chi-restraints excluded: chain F residue 60 TYR Chi-restraints excluded: chain G residue 105 GLU Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain J residue 11 VAL Chi-restraints excluded: chain K residue 20 ILE Chi-restraints excluded: chain K residue 23 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 177 optimal weight: 0.7980 chunk 51 optimal weight: 5.9990 chunk 401 optimal weight: 0.9990 chunk 340 optimal weight: 20.0000 chunk 403 optimal weight: 30.0000 chunk 230 optimal weight: 7.9990 chunk 345 optimal weight: 5.9990 chunk 92 optimal weight: 0.9990 chunk 246 optimal weight: 1.9990 chunk 280 optimal weight: 0.6980 chunk 160 optimal weight: 0.9980 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 957 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4249 r_free = 0.4249 target = 0.139625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.082773 restraints weight = 85192.170| |-----------------------------------------------------------------------------| r_work (start): 0.3129 rms_B_bonded: 3.40 r_work: 0.2963 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2940 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2940 r_free = 0.2940 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2940 r_free = 0.2940 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.2940 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8648 moved from start: 0.2059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 34089 Z= 0.121 Angle : 0.624 41.543 46473 Z= 0.308 Chirality : 0.043 0.195 5308 Planarity : 0.004 0.094 5918 Dihedral : 5.170 57.232 5420 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.97 % Favored : 93.86 % Rotamer: Outliers : 1.38 % Allowed : 14.16 % Favored : 84.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.90 (0.13), residues: 4139 helix: 2.43 (0.21), residues: 654 sheet: -0.06 (0.17), residues: 982 loop : -1.77 (0.11), residues: 2503 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG G 103 TYR 0.026 0.001 TYR B 265 PHE 0.015 0.001 PHE B 347 TRP 0.025 0.001 TRP F 47 HIS 0.005 0.001 HIS F 35 Details of bonding type rmsd covalent geometry : bond 0.00280 (33997) covalent geometry : angle 0.61540 (46247) SS BOND : bond 0.00361 ( 50) SS BOND : angle 1.25690 ( 100) hydrogen bonds : bond 0.04768 ( 1043) hydrogen bonds : angle 4.68833 ( 2970) link_BETA1-3 : bond 0.00640 ( 1) link_BETA1-3 : angle 1.30916 ( 3) link_BETA1-4 : bond 0.00380 ( 8) link_BETA1-4 : angle 1.33782 ( 24) link_NAG-ASN : bond 0.00193 ( 33) link_NAG-ASN : angle 2.01441 ( 99) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17028.52 seconds wall clock time: 289 minutes 10.95 seconds (17350.95 seconds total)